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Santacruz CA, Vincent JL, Duitama J, Bautista E, Imbault V, Bruneau M, Creteur J, Brimioulle S, Communi D, Taccone FS. vCSF Danger-associated Molecular Patterns After Traumatic and Nontraumatic Acute Brain Injury: A Prospective Study. J Neurosurg Anesthesiol 2024; 36:252-257. [PMID: 37188652 DOI: 10.1097/ana.0000000000000916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 03/14/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Danger-associated molecular patterns (DAMPs) may be implicated in the pathophysiological pathways associated with an unfavorable outcome after acute brain injury (ABI). METHODS We collected samples of ventricular cerebrospinal fluid (vCSF) for 5 days in 50 consecutive patients at risk of intracranial hypertension after traumatic and nontraumatic ABI. Differences in vCSF protein expression over time were evaluated using linear models and selected for functional network analysis using the PANTHER and STRING databases. The primary exposure of interest was the type of brain injury (traumatic vs. nontraumatic), and the primary outcome was the vCSF expression of DAMPs. Secondary exposures of interest included the occurrence of intracranial pressure ≥20 or ≥ 30 mm Hg during the 5 days post-ABI, intensive care unit (ICU) mortality, and neurological outcome (assessed using the Glasgow Outcome Score) at 3 months post-ICU discharge. Secondary outcomes included associations of these exposures with the vCSF expression of DAMPs. RESULTS A network of 6 DAMPs ( DAMP_trauma ; protein-protein interaction [PPI] P =0.04) was differentially expressed in patients with ABI of traumatic origin compared with those with nontraumatic ABI. ABI patients with intracranial pressure ≥30 mm Hg differentially expressed a set of 38 DAMPS ( DAMP_ICP30 ; PPI P < 0.001). Proteins in DAMP_ICP30 are involved in cellular proteolysis, complement pathway activation, and post-translational modifications. There were no relationships between DAMP expression and ICU mortality or unfavorable versus favorable outcomes. CONCLUSIONS Specific patterns of vCSF DAMP expression differentiated between traumatic and nontraumatic types of ABI and were associated with increased episodes of severe intracranial hypertension.
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Affiliation(s)
- Carlos A Santacruz
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
- Department of Intensive and Critical Care Medicine, Santa Fe de Bogotá Foundation
| | - Jean-Louis Vincent
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jorge Duitama
- Systems and Computing Engineering Department, University of los Andes, Bogotá, Colombia
| | - Edwin Bautista
- Department of Intensive and Critical Care Medicine, Santa Fe de Bogotá Foundation
| | - Virginie Imbault
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Michael Bruneau
- Department of Neurosurgery, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques Creteur
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Serge Brimioulle
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - David Communi
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabio S Taccone
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
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Lange E, Kranert L, Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol 2024; 15:1368377. [PMID: 38962127 PMCID: PMC11220171 DOI: 10.3389/fmicb.2024.1368377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.
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Affiliation(s)
- Emanuel Lange
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Lena Kranert
- Institute for Automation Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jacob Krüger
- Engineering of Software-Intensive Systems, Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Dirk Benndorf
- Applied Biosciences and Bioprocess Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Robert Heyer
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Multidimensional Omics Data Analysis, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Rydén M, Sjögren A, Önnerfjord P, Turkiewicz A, Tjörnstrand J, Englund M, Ali N. Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid. Mol Cell Proteomics 2024; 23:100785. [PMID: 38750696 PMCID: PMC11252953 DOI: 10.1016/j.mcpro.2024.100785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/17/2024] [Accepted: 05/11/2024] [Indexed: 06/23/2024] Open
Abstract
The molecular mechanisms that drive the onset and development of osteoarthritis (OA) remain largely unknown. In this exploratory study, we used a proteomic platform (SOMAscan assay) to measure the relative abundance of more than 6000 proteins in synovial fluid (SF) from knees of human donors with healthy or mildly degenerated tissues, and knees with late-stage OA from patients undergoing knee replacement surgery. Using a linear mixed effects model, we estimated the differential abundance of 6251 proteins between the three groups. We found 583 proteins upregulated in the late-stage OA, including MMP1, collagenase 3 and interleukin-6. Further, we selected 760 proteins (800 aptamers) based on absolute fold changes between the healthy and mild degeneration groups. To those, we applied Gaussian Graphical Models (GGMs) to analyze the conditional dependence of proteins and to identify key proteins and subnetworks involved in early OA pathogenesis. After regularization and stability selection, we identified 102 proteins involved in GGM networks. Notably, network complexity was lost in the protein graph for mild degeneration when compared to controls, suggesting a disruption in the regular protein interplay. Furthermore, among our main findings were several downregulated (in mild degeneration versus healthy) proteins with unique interactions in the healthy group, one of which, SLCO5A1, has not previously been associated with OA. Our results suggest that this protein is important for healthy joint function. Further, our data suggests that SF proteomics, combined with GGMs, can reveal novel insights into the molecular pathogenesis and identification of biomarker candidates for early-stage OA.
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Affiliation(s)
- Martin Rydén
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Amanda Sjögren
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden.
| | - Patrik Önnerfjord
- Department of Clinical Sciences Lund, Rheumatology, Rheumatology and Molecular Skeletal Biology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Aleksandra Turkiewicz
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Jon Tjörnstrand
- Department of Orthopaedics, Skåne University Hospital, Lund, Sweden
| | - Martin Englund
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Neserin Ali
- Clinical Epidemiology Unit, Department of Clinical Sciences Lund, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
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Reis FJJ, Bonfim IDS, Corrêa LA, Nogueira LC, Meziat-Filho N, Almeida RSD. Uncovering emotional and network dynamics in the speech of patients with chronic low back pain. Musculoskelet Sci Pract 2024; 70:102925. [PMID: 38430821 DOI: 10.1016/j.msksp.2024.102925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/26/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Computational linguistics allows an understanding of language structure and different forms of expression of patients' perceptions. AIMS The aims of this study were (i) to carry out a descriptive analysis of the discourse of people with chronic low back pain using sentiment analysis (SA) and network analysis; (ii) to verify the correlation between patients' profiles, pain intensity and disability levels with SA and network analysis; and (iii) to identify clusters in our sample according to language and SA using an unsupervised machine learning technique. METHODS We performed a secondary analysis of a qualitative study including participants with chronic non-specific low back pain. We used the data related to participants' feelings when they received the diagnosis. The SA and network analysis were performed using the Valence Aware Dictionary and sEntiment Reasoner, and the Speech Graph, respectively. Clustering was performed using the K-means algorithm. RESULTS In the SA, the mean composite score was -0.31 (Sd. = 0.58). Most participants presented a negative discourse (n = 41; 72%). Word Count (WC) and Largest Strongly connected Component (LSC) positively correlated with education. No statistically significant correlations were observed between pain intensity, disability levels, SA, and network analysis. Two clusters were identified in our sample. CONCLUSION The SA showed that participants reported their feeling when describing the moment of the diagnosis using sentences with negative discourse. We did not find a statistically significant correlation between pain intensity, disability levels, SA, and network analysis. Education level presented positive correlation with WC and LSC.
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Affiliation(s)
- Felipe J J Reis
- Physical Therapy Department, Instituto Federal do Rio de Janeiro (IFRJ), Rio de Janeiro, RJ, Brazil; Pain in Motion Research Group, Department of Physiotherapy, Human Physiology and Anatomy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Igor da Silva Bonfim
- Postgraduate Program in Rehabilitation Sciences, Centro Universitário Augusto Motta (UNISUAM), Rio de Janeiro, RJ, Brazil
| | - Leticia Amaral Corrêa
- Department of Chiropractic, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Leandro Calazans Nogueira
- Physical Therapy Department, Instituto Federal do Rio de Janeiro (IFRJ), Rio de Janeiro, RJ, Brazil; Postgraduate Program in Rehabilitation Sciences, Centro Universitário Augusto Motta (UNISUAM), Rio de Janeiro, RJ, Brazil
| | - Ney Meziat-Filho
- Postgraduate Program in Rehabilitation Sciences, Centro Universitário Augusto Motta (UNISUAM), Rio de Janeiro, RJ, Brazil
| | - Renato Santos de Almeida
- Physical Therapy Department, Instituto Federal do Rio de Janeiro (IFRJ), Rio de Janeiro, RJ, Brazil; Postgraduate Program in Rehabilitation Sciences, Centro Universitário Augusto Motta (UNISUAM), Rio de Janeiro, RJ, Brazil
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Du Y, Nie J, Zhang J, Fang Y, Wei W, Wang J, Zhang S, Wang J, Li X. Disrupted topological organization of the default mode network in mild cognitive impairment with subsyndromal depression: A graph theoretical analysis. CNS Neurosci Ther 2024; 30:e14547. [PMID: 38105496 PMCID: PMC11017411 DOI: 10.1111/cns.14547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 10/26/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
AIMS Subsyndromal depression (SSD) is common in mild cognitive impairment (MCI). However, the neural mechanisms underlying MCI with SSD (MCID) are unclear. The default mode network (DMN) is associated with cognitive processes and depressive symptoms. Therefore, we aimed to explore the topological organization of the DMN in patients with MCID. METHODS Forty-two MCID patients, 34 MCI patients without SSD (MCIND), and 36 matched healthy controls (HCs) were enrolled. The resting-state functional connectivity of the DMN of the participants was analyzed using a graph theoretical approach. Correlation analyses of network topological metrics, depressive symptoms, and cognitive function were conducted. Moreover, support vector machine (SVM) models were constructed based on topological metrics to distinguish MCID from MCIND. Finally, we used 10 repeats of 5-fold cross-validation for performance verification. RESULTS We found that the global efficiency and nodal efficiency of the left anterior medial prefrontal cortex (aMPFC) of the MCID group were significantly lower than the MCIND group. Moreover, small-worldness and global efficiency were negatively correlated with depressive symptoms in MCID, and the nodal efficiency of the left lateral temporal cortex and left aMPFC was positively correlated with cognitive function in MCID. In cross-validation, the SVM model had an accuracy of 0.83 [95% CI 0.79-0.87], a sensitivity of 0.88 [95% CI 0.86-0.90], a specificity of 0.75 [95% CI 0.72-0.78] and an area under the curve of 0.88 [95% CI 0.85-0.91]. CONCLUSIONS The coexistence of MCI and SSD was associated with the greatest disrupted topological organization of the DMN. The network topological metrics could identify MCID and serve as biomarkers of different clinical phenotypic presentations of MCI.
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Affiliation(s)
- Yang Du
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jing Nie
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jian‐Ye Zhang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuan Fang
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Wen‐Jing Wei
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jing‐Hua Wang
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Shao‐Wei Zhang
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jin‐Hong Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xia Li
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
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Ray AK, Priya A, Malik MZ, Thanaraj TA, Singh AK, Mago P, Ghosh C, Shalimar, Tandon R, Chaturvedi R. A bioinformatics approach to elucidate conserved genes and pathways in C. elegans as an animal model for cardiovascular research. Sci Rep 2024; 14:7471. [PMID: 38553458 PMCID: PMC10980734 DOI: 10.1038/s41598-024-56562-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in CVD research. Caenorhabditis elegans, a nematode species, has emerged as a prominent experimental organism widely utilized in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilization for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signaling pathway, the FoxO signaling pathway, the MAPK signaling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.
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Affiliation(s)
- Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, India.
| | - Anjali Priya
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Md Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait.
| | | | - Alok Kumar Singh
- Department of Zoology, Ramjas College, University of Delhi, New Delhi, India
| | - Payal Mago
- Shaheed Rajguru College of Applied Science for Women, University of Delhi, New Delhi, India
- Campus of Open Learning, University of Delhi, New Delhi, India
| | - Chirashree Ghosh
- Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Shalimar
- Department of Gastroenterology, All India Institute of Medical Science, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Cain JY, Evarts JI, Yu JS, Bagheri N. Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae131. [PMID: 38444088 PMCID: PMC10957516 DOI: 10.1093/bioinformatics/btae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/08/2024] [Accepted: 03/01/2024] [Indexed: 03/07/2024]
Abstract
MOTIVATION Emergent biological dynamics derive from the evolution of lower-level spatial and temporal processes. A long-standing challenge for scientists and engineers is identifying simple low-level rules that give rise to complex higher-level dynamics. High-resolution biological data acquisition enables this identification and has evolved at a rapid pace for both experimental and computational approaches. Simultaneously harnessing the resolution and managing the expense of emerging technologies-e.g. live cell imaging, scRNAseq, agent-based models-requires a deeper understanding of how spatial and temporal axes impact biological systems. Effective emulation is a promising solution to manage the expense of increasingly complex high-resolution computational models. In this research, we focus on the emulation of a tumor microenvironment agent-based model to examine the relationship between spatial and temporal environment features, and emergent tumor properties. RESULTS Despite significant feature engineering, we find limited predictive capacity of tumor properties from initial system representations. However, incorporating temporal information derived from intermediate simulation states dramatically improves the predictive performance of machine learning models. We train a deep-learning emulator on intermediate simulation states and observe promising enhancements over emulators trained solely on initial conditions. Our results underscore the importance of incorporating temporal information in the evaluation of spatio-temporal emergent behavior. Nevertheless, the emulators exhibit inconsistent performance, suggesting that the underlying model characterizes unique cell populations dynamics that are not easily replaced. AVAILABILITY AND IMPLEMENTATION All source codes for the agent-based model, emulation, and analyses are publicly available at the corresponding DOIs: 10.5281/zenodo.10622155, 10.5281/zenodo.10611675, 10.5281/zenodo.10621244, respectively.
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Affiliation(s)
- Jason Y Cain
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, United States
| | - Jacob I Evarts
- Department of Biology, University of Washington, Seattle, WA 98195, United States
| | - Jessica S Yu
- Department of Biology, University of Washington, Seattle, WA 98195, United States
| | - Neda Bagheri
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, United States
- Department of Biology, University of Washington, Seattle, WA 98195, United States
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Feng H, Cottrell S, Hozumi Y, Wei GW. Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data. Comput Biol Med 2024; 171:108211. [PMID: 38422960 PMCID: PMC10965033 DOI: 10.1016/j.compbiomed.2024.108211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/02/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expression dynamics. scRNA-seq analysis represents a challenging and cutting-edge frontier within the field of biological research. Differential geometry serves as a powerful mathematical tool in various applications of scientific research. In this study, we introduce, for the first time, a multiscale differential geometry (MDG) strategy for addressing the challenges encountered in scRNA-seq data analysis. We assume that intrinsic properties of cells lie on a family of low-dimensional manifolds embedded in the high-dimensional space of scRNA-seq data. Multiscale cell-cell interactive manifolds are constructed to reveal complex relationships in the cell-cell network, where curvature-based features for cells can decipher the intricate structural and biological information. We showcase the utility of our novel approach by demonstrating its effectiveness in classifying cell types. This innovative application of differential geometry in scRNA-seq analysis opens new avenues for understanding the intricacies of biological networks and holds great potential for network analysis in other fields.
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Affiliation(s)
- Hongsong Feng
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Sean Cottrell
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Yuta Hozumi
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA; Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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9
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Cummings MJ, Bakamutumaho B, Lutwama JJ, Owor N, Che X, Astorkia M, Postler TS, Kayiwa J, Kiconco J, Muwanga M, Nsereko C, Rwamutwe E, Nayiga I, Kyebambe S, Haumba M, Bosa HK, Ocom F, Watyaba B, Kikaire B, Tomoiaga AS, Kisaka S, Kiwanuka N, Lipkin WI, O'Donnell MR. COVID-19 immune signatures in Uganda persist in HIV co-infection and diverge by pandemic phase. Nat Commun 2024; 15:1475. [PMID: 38368384 PMCID: PMC10874401 DOI: 10.1038/s41467-024-45204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/17/2024] [Indexed: 02/19/2024] Open
Abstract
Little is known about the pathobiology of SARS-CoV-2 infection in sub-Saharan Africa, where severe COVID-19 fatality rates are among the highest in the world and the immunological landscape is unique. In a prospective cohort study of 306 adults encompassing the entire clinical spectrum of SARS-CoV-2 infection in Uganda, we profile the peripheral blood proteome and transcriptome to characterize the immunopathology of COVID-19 across multiple phases of the pandemic. Beyond the prognostic importance of myeloid cell-driven immune activation and lymphopenia, we show that multifaceted impairment of host protein synthesis and redox imbalance define core biological signatures of severe COVID-19, with central roles for IL-7, IL-15, and lymphotoxin-α in COVID-19 respiratory failure. While prognostic signatures are generally consistent in SARS-CoV-2/HIV-coinfection, type I interferon responses uniquely scale with COVID-19 severity in persons living with HIV. Throughout the pandemic, COVID-19 severity peaked during phases dominated by A.23/A.23.1 and Delta B.1.617.2/AY variants. Independent of clinical severity, Delta phase COVID-19 is distinguished by exaggerated pro-inflammatory myeloid cell and inflammasome activation, NK and CD8+ T cell depletion, and impaired host protein synthesis. Combining these analyses with a contemporary Ugandan cohort of adults hospitalized with influenza and other severe acute respiratory infections, we show that activation of epidermal and platelet-derived growth factor pathways are distinct features of COVID-19, deepening translational understanding of mechanisms potentially underlying SARS-CoV-2-associated pulmonary fibrosis. Collectively, our findings provide biological rationale for use of broad and targeted immunotherapies for severe COVID-19 in sub-Saharan Africa, illustrate the relevance of local viral and host factors to SARS-CoV-2 immunopathology, and highlight underemphasized yet therapeutically exploitable immune pathways driving COVID-19 severity.
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Affiliation(s)
- Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maider Astorkia
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jocelyn Kiconco
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | | | - Irene Nayiga
- Entebbe Regional Referral Hospital, Entebbe, Uganda
| | | | - Mercy Haumba
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Kyobe Bosa
- Uganda Peoples' Defence Forces, Kampala, Uganda
- Ministry of Health, Kampala, Uganda
| | | | - Benjamin Watyaba
- European and Developing Countries Clinical Trials Partnership-Eastern Africa Consortium for Clinical Research, Uganda Virus Research Institute, Entebbe, Uganda
| | - Bernard Kikaire
- European and Developing Countries Clinical Trials Partnership-Eastern Africa Consortium for Clinical Research, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Pediatrics, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alin S Tomoiaga
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Accounting, Business Analytics, Computer Information Systems, and Law, Manhattan College, New York, NY, USA
| | - Stevens Kisaka
- Department of Epidemiology and Biostatistics, Makerere University School of Public Health, Kampala, Uganda
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, Makerere University School of Public Health, Kampala, Uganda
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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10
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Kole A, Bag AK, Pal AJ, De D. Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology. BMC Bioinformatics 2024; 25:74. [PMID: 38365632 PMCID: PMC10874019 DOI: 10.1186/s12859-024-05690-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
PURPOSE Graph coloring approach has emerged as a valuable problem-solving tool for both theoretical and practical aspects across various scientific disciplines, including biology. In this study, we demonstrate the graph coloring's effectiveness in computational network biology, more precisely in analyzing protein-protein interaction (PPI) networks to gain insights about the viral infections and its consequences on human health. Accordingly, we propose a generic model that can highlight important hub proteins of virus-associated disease manifestations, changes in disease-associated biological pathways, potential drug targets and respective drugs. We test our model on SARS-CoV-2 infection, a highly transmissible virus responsible for the COVID-19 pandemic. The pandemic took significant human lives, causing severe respiratory illnesses and exhibiting various symptoms ranging from fever and cough to gastrointestinal, cardiac, renal, neurological, and other manifestations. METHODS To investigate the underlying mechanisms of SARS-CoV-2 infection-induced dysregulation of human pathobiology, we construct a two-level PPI network and employed a differential evolution-based graph coloring (DEGCP) algorithm to identify critical hub proteins that might serve as potential targets for resolving the associated issues. Initially, we concentrate on the direct human interactors of SARS-CoV-2 proteins to construct the first-level PPI network and subsequently applied the DEGCP algorithm to identify essential hub proteins within this network. We then build a second-level PPI network by incorporating the next-level human interactors of the first-level hub proteins and use the DEGCP algorithm to predict the second level of hub proteins. RESULTS We first identify the potential crucial hub proteins associated with SARS-CoV-2 infection at different levels. Through comprehensive analysis, we then investigate the cellular localization, interactions with other viral families, involvement in biological pathways and processes, functional attributes, gene regulation capabilities as transcription factors, and their associations with disease-associated symptoms of these identified hub proteins. Our findings highlight the significance of these hub proteins and their intricate connections with disease pathophysiology. Furthermore, we predict potential drug targets among the hub proteins and identify specific drugs that hold promise in preventing or treating SARS-CoV-2 infection and its consequences. CONCLUSION Our generic model demonstrates the effectiveness of DEGCP algorithm in analyzing biological PPI networks, provides valuable insights into disease biology, and offers a basis for developing novel therapeutic strategies for other viral infections that may cause future pandemic.
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Affiliation(s)
- Arnab Kole
- Department of Computer Application, The Heritage Academy, Kolkata, W.B., 700107, India.
| | - Arup Kumar Bag
- Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | | | - Debashis De
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Nadia, W.B., 741249, India
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11
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Castaneda EU, Baker EJ. KNeXT: a NetworkX-based topologically relevant KEGG parser. Front Genet 2024; 15:1292394. [PMID: 38415058 PMCID: PMC10896898 DOI: 10.3389/fgene.2024.1292394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
Automating the recreation of gene and mixed gene-compound networks from Kyoto Encyclopedia of Genes and Genomes (KEGG) Markup Language (KGML) files is challenging because the data structure does not preserve the independent or loosely connected neighborhoods in which they were originally derived, referred to here as its topological environment. Identical accession numbers may overlap, causing neighborhoods to artificially collapse based on duplicated identifiers. This causes current parsers to create misleading or erroneous graphical representations when mixed gene networks are converted to gene-only networks. To overcome these challenges we created a python-based KEGG NetworkX Topological (KNeXT) parser that allows users to accurately recapitulate genetic networks and mixed networks from KGML map data. The software, archived as a python package index (PyPI) file to ensure broad application, is designed to ingest KGML files through built-in APIs and dynamically create high-fidelity topological representations. The utilization of NetworkX's framework to generate tab-separated files additionally ensures that KNeXT results may be imported into other graph frameworks and maintain programmatic access to the original x-y axis positions to each node in the KEGG pathway. KNeXT is a well-described Python 3 package that allows users to rapidly download and aggregate specific KGML files and recreate KEGG pathways based on a range of user-defined settings. KNeXT is platform-independent, distinctive, and it is not written on top of other Python parsers. Furthermore, KNeXT enables users to parse entire local folders or single files through command line scripts and convert the output into NCBI or UniProt IDs. KNeXT provides an ability for researchers to generate pathway visualizations while persevering the original context of a KEGG pathway. Source code is freely available at https://github.com/everest-castaneda/knext.
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Affiliation(s)
- Everest Uriel Castaneda
- Department of Biology, Baylor University, Waco, TX, United States
- School of Engineering and Computer Science, Baylor University, Waco, TX, United States
| | - Erich J Baker
- Department of Mathematics and Computer Science, Belmont University, Nashville, TN, United States
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12
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Pravallika G, Rajasekaran R. Stage II oesophageal carcinoma: peril in disguise associated with cellular reprogramming and oncogenesis regulated by pseudogenes. BMC Genomics 2024; 25:135. [PMID: 38308202 PMCID: PMC10835973 DOI: 10.1186/s12864-024-10023-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/17/2024] [Indexed: 02/04/2024] Open
Abstract
INTRODUCTION Pseudogenes have been implicated for their role in regulating cellular differentiation and organismal development. However, their role in promoting cancer-associated differentiation has not been well-studied. This study explores the tumour landscape of oesophageal carcinoma to identify pseudogenes that may regulate events of differentiation to promote oncogenic transformation. MATERIALS AND METHOD De-regulated differentiation-associated pseudogenes were identified using DeSeq2 followed by 'InteractiVenn' analysis to identify their expression pattern. Gene expression dependent and independent enrichment analyses were performed with GSEA and ShinyGO, respectively, followed by quantification of cellular reprogramming, extent of differentiation and pleiotropy using three unique metrics. Stage-specific gene regulatory networks using Bayesian Network Splitting Average were generated, followed by network topology analysis. MEME, STREME and Tomtom were employed to identify transcription factors and miRNAs that play a regulatory role downstream of pseudogenes to initiate cellular reprogramming and further promote oncogenic transformation. The patient samples were stratified based on the expression pattern of pseudogenes, followed by GSEA, mutation analysis and survival analysis using GSEA, MAF and 'survminer', respectively. RESULTS Pseudogenes display a unique stage-wise expression pattern that characterizes stage II (SII) ESCA with a high rate of cellular reprogramming, degree of differentiation and pleiotropy. Gene regulatory network and associated topology indicate high robustness, thus validating high pleiotropy observed for SII. Pseudogene-regulated expression of SOX2, FEV, PRRX1 and TFAP2A in SII may modulate cellular reprogramming and promote oncogenesis. Additionally, patient stratification-based mutational analysis in SII signifies APOBEC3A (A3A) as a potential hallmark of homeostatic mutational events of reprogrammed cells which in addition to de-regulated APOBEC3G leads to distinct events of hypermutations. Further enrichment analysis for both cohorts revealed the critical role of combinatorial expression of pseudogenes in cellular reprogramming. Finally, survival analysis reveals distinct genes that promote poor prognosis in SII ESCA and patient-stratified cohorts, thus providing valuable prognostic bio-markers along with markers of differentiation and oncogenesis for distinct landscapes of pseudogene expression. CONCLUSION Pseudogenes associated with the events of differentiation potentially aid in the initiation of cellular reprogramming to facilitate oncogenic transformation, especially during SII ESCA. Despite a better overall survival of SII, patient stratification reveals combinatorial de-regulation of pseudogenes as a notable marker for a high degree of cellular differentiation with a unique mutational landscape.
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Affiliation(s)
- Govada Pravallika
- Quantitative Biology Lab, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramalingam Rajasekaran
- Quantitative Biology Lab, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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13
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Poorinmohammad N, Salavati R. Prioritization of Trypanosoma brucei editosome protein interactions interfaces at residue resolution through proteome-scale network analysis. BMC Mol Cell Biol 2024; 25:3. [PMID: 38279116 PMCID: PMC10811811 DOI: 10.1186/s12860-024-00499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Trypanosoma brucei is the causative agent for trypanosomiasis in humans and livestock, which presents a growing challenge due to drug resistance. While identifying novel drug targets is vital, the process is delayed due to a lack of functional information on many of the pathogen's proteins. Accordingly, this paper presents a computational framework for prioritizing drug targets within the editosome, a vital molecular machinery responsible for mitochondrial RNA processing in T. brucei. Importantly, this framework may eliminate the need for prior gene or protein characterization, potentially accelerating drug discovery efforts. RESULTS By integrating protein-protein interaction (PPI) network analysis, PPI structural modeling, and residue interaction network (RIN) analysis, we quantitatively ranked and identified top hub editosome proteins, their key interaction interfaces, and hotspot residues. Our findings were cross-validated and further prioritized by incorporating them into gene set analysis and differential expression analysis of existing quantitative proteomics data across various life stages of T. brucei. In doing so, we highlighted PPIs such as KREL2-KREPA1, RESC2-RESC1, RESC12A-RESC13, and RESC10-RESC6 as top candidates for further investigation. This includes examining their interfaces and hotspot residues, which could guide drug candidate selection and functional studies. CONCLUSION RNA editing offers promise for target-based drug discovery, particularly with proteins and interfaces that play central roles in the pathogen's life cycle. This study introduces an integrative drug target identification workflow combining information from the PPI network, PPI 3D structure, and reside-level information of their interface which can be applicable to diverse pathogens. In the case of T. brucei, via this pipeline, the present study suggested potential drug targets with residue-resolution from RNA editing machinery. However, experimental validation is needed to fully realize its potential in advancing urgently needed antiparasitic drug development.
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Affiliation(s)
- Naghmeh Poorinmohammad
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Montreal, Quebec, H9X 3V9, Canada
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Montreal, Quebec, H9X 3V9, Canada.
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada.
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14
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Ebrahimi A, Roshani F. Systems biology approaches to identify driver genes and drug combinations for treating COVID-19. Sci Rep 2024; 14:2257. [PMID: 38278931 PMCID: PMC10817985 DOI: 10.1038/s41598-024-52484-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Corona virus 19 (Covid-19) has caused many problems in public health, economic, and even cultural and social fields since the beginning of the epidemic. However, in order to provide therapeutic solutions, many researches have been conducted and various omics data have been published. But there is still no early diagnosis method and comprehensive treatment solution. In this manuscript, by collecting important genes related to COVID-19 and using centrality and controllability analysis in PPI networks and signaling pathways related to the disease; hub and driver genes have been identified in the formation and progression of the disease. Next, by analyzing the expression data, the obtained genes have been evaluated. The results show that in addition to the significant difference in the expression of most of these genes, their expression correlation pattern is also different in the two groups of COVID-19 and control. Finally, based on the drug-gene interaction, drugs affecting the identified genes are presented in the form of a bipartite graph, which can be used as the potential drug combinations.
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Affiliation(s)
- Ali Ebrahimi
- Department of Physics, Alzahra University, Tehran, Iran
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15
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Ray AK, Priya A, Malik MZ, Thanaraj TA, Singh AK, Mago P, Ghosh C, Shalimar, Tandon R, Chaturvedi R. Conserved Cardiovascular Network: Bioinformatics Insights into Genes and Pathways for Establishing Caenorhabditis elegans as an Animal Model for Cardiovascular Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.24.573256. [PMID: 38234826 PMCID: PMC10793405 DOI: 10.1101/2023.12.24.573256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in cardiovascular disease (CVD) research. Caenorhabditis elegans , a nematode species, has emerged as a prominent experimental organism widely utilised in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilisation for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signalling pathway, the FoxO signalling pathway, the MAPK signalling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.
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16
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K I, Y M, A N, D S, G G, R S, D G, V SN, O S, M F, S R, S O, J MG, A M. Cognitive behavioral and mindfulness with daily exercise intervention is associated with changes in intestinal microbial taxa and systemic inflammation in patients with Crohn's disease. Gut Microbes 2024; 16:2337269. [PMID: 38591914 PMCID: PMC11005811 DOI: 10.1080/19490976.2024.2337269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease associated with psychological distress and intestinal microbial changes. Here, we examined whether a 3-month period of Cognitive Behavioral and Mindfulness with Daily Exercise (COBMINDEX) intervention, which improves the wellbeing and inflammatory state of CD patients, may also affect their gut microbiome. Gut microbiota, circulating inflammatory markers and hormones were analyzed in 24 CD patients before (T1) and after 3 months of COBMINDEX (T2), and in 25 age- and sex-matched wait-list control patients at the corresponding time-points. Microbiota analysis examined relative taxonomical abundance, alpha and beta diversity, and microbiome correlations with inflammatory and psychological parameters. At T1, CD patients exhibited a characteristic microbial profile mainly constituted of Proteobacteria (17.71%), Firmicutes (65.56%), Actinobacteria (8.46%) and Bacteroidetes (6.24%). Baseline bacterial abundances showed significant correlations with psychological markers of distress and with IFNγ . Following COBMINDEX, no significant changes in alpha and beta diversity were observed between both study groups, though a trend change in beta diversity was noted. Significant changes occurred in the abundance of phyla, families and genera only among the COBMINDEX group. Furthermore, abundance of phyla, families and genera that were altered following COBMNIDEX, significantly correlated with levels of cytokines and psychological parameters. Our results demonstrated that a short-term intervention of COBMINDEX was associated with changes in microbial indices, some of which are linked to psychological manifestations and systemic inflammation in CD patients. Psychological interventions to reduce chronic stress, such as COBMINDEX, appear to be beneficial in mitigating the pathobiology of CD patients, and may thus provide a useful adjunct to pharmacological therapy.
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Affiliation(s)
- Ilan K
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Motro Y
- MAGICAL Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva, Israel
| | - Nemirovsky A
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Schwartz D
- Department of Gastroenterology and Hepatology, Soroka Medical Center, and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Goren G
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sergienko R
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Greenberg D
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Slonim-Nevo V
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sarid O
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Friger M
- Department of Epidemiology, Biostatistics and Community Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Regev S
- Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Odes S
- Department of Gastroenterology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Moran-Gilad J
- MAGICAL Group, Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben‐Gurion University of the Negev, Beer‐Sheva, Israel
| | - Monsonego A
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The National Institute of Biotechnology in the Negev, School of Brain Sciences and Cognition, and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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17
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Lee C, Wei S, McConnell ES, Tsumura H, Xue TM, Pan W. Comorbidity Patterns in Older Patients Undergoing Hip Fracture Surgery: A Comorbidity Network Analysis Study. Clin Nurs Res 2024; 33:70-80. [PMID: 37932937 DOI: 10.1177/10547738231209367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Comorbidity network analysis (CNA) is a technique in which mathematical graphs encode correlations (edges) among diseases (nodes) inferred from the disease co-occurrence data of a patient group. The present study applied this network-based approach to identifying comorbidity patterns in older patients undergoing hip fracture surgery. This was a retrospective observational cohort study using electronic health records (EHR). EHR data were extracted from the one University Health System in the southeast United States. The cohort included patients aged 65 and above who had a first-time low-energy traumatic hip fracture treated surgically between October 1, 2015 and December 31, 2018 (n = 1,171). Comorbidity includes 17 diagnoses classified by the Charlson Comorbidity Index. The CNA investigated the comorbid associations among 17 diagnoses. The association strength was quantified using the observed-to-expected ratio (OER). Several network centrality measures were used to examine the importance of nodes, namely degree, strength, closeness, and betweenness centrality. A cluster detection algorithm was employed to determine specific clusters of comorbidities. Twelve diseases were significantly interconnected in the network (OER > 1, p-value < .05). The most robust associations were between metastatic carcinoma and mild liver disease, myocardial infarction and congestive heart failure, and hemi/paraplegia and cerebrovascular disease (OER > 2.5). Cerebrovascular disease, congestive heart failure, and myocardial infarction were identified as the central diseases that co-occurred with numerous other diseases. Two distinct clusters were noted, and the largest cluster comprised 10 diseases, primarily encompassing cardiometabolic and cognitive disorders. The results highlight specific patient comorbidities that could be used to guide clinical assessment, management, and targeted interventions that improve hip fracture outcomes in this patient group.
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Affiliation(s)
- Chiyoung Lee
- School of Nursing & Health Studies, University of Washington Bothell, Bothell, WA, USA
| | - Sijia Wei
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Eleanor S McConnell
- Duke University School of Nursing, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
| | | | - Tingzhong Michelle Xue
- Duke University School of Nursing, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
| | - Wei Pan
- Duke University School of Nursing, Durham, NC, USA
- Duke University School of Medicine, Durham, NC, USA
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18
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Ullah A, Bano Z, Zaman S. Computational aspects of two important biochemical networks with respect to some novel molecular descriptors. J Biomol Struct Dyn 2024; 42:791-805. [PMID: 37000943 DOI: 10.1080/07391102.2023.2195944] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Quantitative structure-activity relationship (QSAR) represents quantitative correlation of biological structural features (called as topological indices) and pharmacological activity as response endpoints. Topological index is a molecular descriptor extensively used to study QSAR of pharmaceutical to assess their molecular characteristics by numerical computation. Meanwhile, the topological indices are numerical functions which are used to predict the growth rate of microorganisms in biological networks. Theoretical assessment of microorganism, such as bacteria and viruses help to expedite the vaccine design and discovery process by rationalizing the lead identification, lead optimization and understanding their mechanism of actions. Hypertree, a network structure derived from graph theory, has a great importance in biological networks for growth of microorganisms, such as bacteria and viruses. In this article, some novel eccentric and degree based topological features of two important biological networks (hypertree and its corona product) are obtained on h-level and derived closed formulas for them. Based on the obtained topological features, the biological properties of these networks are investigated.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Mathematical Sciences, Karakoram International University, Gilgit, Pakistan
| | - Zohra Bano
- Department of Mathematical Sciences, Karakoram International University, Gilgit, Pakistan
| | - Shahid Zaman
- Department of Mathematics, University of Sialkot, Sialkot, Pakistan
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19
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Miao X, Shen S, Koch G, Wang X, Li J, Shen X, Qu J, Straubinger RM, Jusko WJ. Systems pharmacodynamic model of combined gemcitabine and trabectedin in pancreatic cancer cells. Part I.Çô Effects on signal transduction pathways related to tumor growth. J Pharm Sci 2024; 113:214-227. [PMID: 38498417 PMCID: PMC11017371 DOI: 10.1016/j.xphs.2023.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/22/2023] [Accepted: 10/22/2023] [Indexed: 03/20/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is often chemotherapy-resistant, and novel drug combinations would fill an unmet clinical need. Previously we reported synergistic cytotoxic effects of gemcitabine and trabectedin on pancreatic cancer cells, but underlying protein-level interaction mechanisms remained unclear. We employed a reliable, sensitive, comprehensive, quantitative, high-throughput IonStar proteomic workflow to investigate the time course of gemcitabine and trabectedin effects, alone and combined, upon pancreatic cancer cells. MiaPaCa-2 cells were incubated with vehicle (controls), gemcitabine, trabectedin, and their combinations over 72 hours. Samples were collected at intervals and analyzed using the label-free IonStar liquid chromatography-mass spectrometry (LC-MS/MS) workflow to provide temporal quantification of protein expression for 4,829 proteins in four experimental groups. To characterize diverse signal transduction pathways, a comprehensive systems pharmacodynamic (SPD) model was developed. The analysis is presented in two parts. Here, Part I describes drug responses in cancer cell growth and migration pathways included in the full model: receptor tyrosine kinase- (RTK), integrin-, G-protein coupled receptor- (GPCR), and calcium-signaling pathways. The developed model revealed multiple underlying mechanisms of drug actions, provides insight into the basis of drug interaction synergism, and offers a scientific rationale for potential drug combination strategies.
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Affiliation(s)
- Xin Miao
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States
| | - Shichen Shen
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States
| | - Gilbert Koch
- Pediatric Pharmacology and Pharmacometrics Research Center, University of Basel, Children's Hospital, Basel, Switzerland
| | - Xue Wang
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States; Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - Jun Li
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States
| | - Xiaomeng Shen
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States
| | - Robert M Straubinger
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States; Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - William J Jusko
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States.
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20
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Karakurt HU, Pir P. SUMA: a lightweight machine learning model-powered shared nearest neighbour-based clustering application interface for scRNA-Seq data. Turk J Biol 2023; 47:413-422. [PMID: 38681777 PMCID: PMC11045205 DOI: 10.55730/1300-0152.2675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/28/2023] [Accepted: 12/18/2023] [Indexed: 05/01/2024] Open
Abstract
Background/aim Single-cell transcriptomics (scRNA-Seq) explores cellular diversity at the gene expression level. Due to the inherent sparsity and noise in scRNA-Seq data and the uncertainty on the types of sequenced cells, effective clustering and cell type annotation are essential. The graph-based clustering of scRNA-Seq data is a simple yet powerful approach that presents data as a "shared nearest neighbour" graph and clusters the cells using graph clustering algorithms. These algorithms are dependent on several user-defined parameters.Here we present SUMA, a lightweight tool that uses a random forest model to predict the optimum number of neighbours to obtain the optimum clustering results. Moreover, we integrated our method with other commonly used methods in an RShiny application. SUMA can be used in a local environment (https://github.com/hkarakurt8742/SUMA) or as a browser tool (https://hkarakurt.shinyapps.io/suma/). Materials and methods Publicly available scRNA-Seq datasets and 3 different graph-based clustering algorithms were used to develop SUMA, and a large range for number of neighbours and variant genes was taken into consideration. The quality of clustering was assessed using the adjusted Rand index (ARI) and true labels of each dataset. The data were split into training and test datasets, and the model was built and optimised using Scikit-learn (Python) and randomForest (R) libraries. Results The accuracy of our machine learning model was 0.96, while the AUC of the ROC curve was 0.98. The model indicated that the number of cells in scRNA-Seq data is the most important feature when deciding the number of neighbours. Conclusion We developed and evaluated the SUMA model and implemented the method in the SUMAShiny app, which integrates SUMA with different clustering methods and enables nonbioinformatician users to cluster and visualise their scRNA data easily. The SUMAShiny app is available both for desktop and browser use.
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Affiliation(s)
- Hamza Umut Karakurt
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Kocaeli, Turkiye
- Idea Technology Solutions R&D Center, İstanbul, Turkiye
| | - Pınar Pir
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Kocaeli, Turkiye
- Idea Technology Solutions R&D Center, İstanbul, Turkiye
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21
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Baron C, Cherkaoui S, Therrien-Laperriere S, Ilboudo Y, Poujol R, Mehanna P, Garrett ME, Telen MJ, Ashley-Koch AE, Bartolucci P, Rioux JD, Lettre G, Rosiers CD, Ruiz M, Hussin JG. Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results. iScience 2023; 26:108473. [PMID: 38077122 PMCID: PMC10709128 DOI: 10.1016/j.isci.2023.108473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/24/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023] Open
Abstract
Metabolite genome-wide association studies (mGWAS) have advanced our understanding of the genetic control of metabolite levels. However, interpreting these associations remains challenging due to a lack of tools to annotate gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we introduce the shortest reactional distance (SRD) metric, drawing from the comprehensive KEGG database, to enhance the biological interpretation of mGWAS results. We applied this approach to three independent mGWAS, including a case study on sickle cell disease patients. Our analysis reveals an enrichment of small SRD values in reported mGWAS pairs, with SRD values significantly correlating with mGWAS p values, even beyond the standard conservative thresholds. We demonstrate the utility of SRD annotation in identifying potential false negatives and inaccuracies within current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs, suitable to integrate statistical evidence to biological networks.
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Affiliation(s)
- Cantin Baron
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Montreal Heart Institute, Montréal, QC, Canada
| | - Sarah Cherkaoui
- Montreal Heart Institute, Montréal, QC, Canada
- Division of Oncology and Children’s Research Center, University Children’s Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France
| | | | - Yann Ilboudo
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Montreal Heart Institute, Montréal, QC, Canada
| | | | | | - Melanie E. Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Marilyn J. Telen
- Division of Hematology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Pablo Bartolucci
- Université Paris Est Créteil, Hôpitaux Universitaires Henri Mondor, APHP, Sickle cell referral center – UMGGR, Créteil, France
- Université Paris Est Créteil, IMRB, Laboratory of excellence LABEX, Créteil, France
| | - John D. Rioux
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Montreal Heart Institute, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Christine Des Rosiers
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Montreal Heart Institute, Montréal, QC, Canada
- Département de Nutrition, Université de Montréal, Montréal, QC, Canada
| | - Matthieu Ruiz
- Montreal Heart Institute, Montréal, QC, Canada
- Département de Nutrition, Université de Montréal, Montréal, QC, Canada
| | - Julie G. Hussin
- Montreal Heart Institute, Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
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22
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Bao Y, Lu P, Wang M, Zhang X, Song A, Gu X, Ma T, Su S, Wang L, Shang X, Zhu Z, Zhai Y, He M, Li Z, Liu H, Fairley CK, Yang J, Zhang L. Exploring multimorbidity profiles in middle-aged inpatients: a network-based comparative study of China and the United Kingdom. BMC Med 2023; 21:495. [PMID: 38093264 PMCID: PMC10720230 DOI: 10.1186/s12916-023-03204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Multimorbidity is better prevented in younger ages than in older ages. This study aims to identify the differences in comorbidity patterns in middle-aged inpatients from China and the United Kingdom (UK). METHODS We utilized 184,133 and 180,497 baseline hospitalization records in middle-aged populations (40-59 years) from Shaanxi, China, and UK Biobank. Logistic regression was used to calculate odds ratios and P values for 43,110 unique comorbidity patterns in Chinese inpatients and 21,026 unique comorbidity patterns in UK inpatients. We included the statistically significant (P values adjusted by Bonferroni correction) and common comorbidity patterns (the pattern with prevalence > 1/10,000 in each dataset) and employed network analysis to construct multimorbidity networks and compare feature differences in multimorbidity networks for Chinese and UK inpatients, respectively. We defined hub diseases as diseases having the top 10 highest number of unique comorbidity patterns in the multimorbidity network. RESULTS We reported that 57.12% of Chinese inpatients had multimorbidity, substantially higher than 30.39% of UK inpatients. The complete multimorbidity network for Chinese inpatients consisted of 1367 comorbidities of 341 diseases and was 2.93 × more complex than that of 467 comorbidities of 215 diseases in the UK. In males, the complexity of the multimorbidity network in China was 2.69 × more than their UK counterparts, while the ratio was 2.63 × in females. Comorbidities associated with hub diseases represented 68.26% of comorbidity frequencies in the complete multimorbidity network in Chinese inpatients and 55.61% in UK inpatients. Essential hypertension, dyslipidemia, type 2 diabetes mellitus, and gastritis and duodenitis were the hub diseases in both populations. The Chinese inpatients consistently demonstrated a higher frequency of comorbidities related to circulatory and endocrine/nutritional/metabolic diseases. In the UK, aside from these comorbidities, comorbidities related to digestive and genitourinary diseases were also prevalent, particularly the latter among female inpatients. CONCLUSIONS Chinese inpatients exhibit higher multimorbidity prevalence and more complex networks compared to their UK counterparts. Multimorbidity with circulatory and endocrine/nutritional/metabolic diseases among both Chinese and UK inpatients necessitates tailored surveillance, prevention, and intervention approaches. Targeted interventions for digestive and genitourinary diseases are warranted for the UK.
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Affiliation(s)
- Yining Bao
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, China
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Pengyi Lu
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, China
| | - Mengjie Wang
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, China
| | - Xueli Zhang
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Aowei Song
- Department of Transfusion Medicine, Shaanxi Provincial People's Hospital, 256 Youyi West Road, Xi'an, 710068, China
| | - Xiaoyun Gu
- Department of Information Technological, Shaanxi Health Information Center, Xi'an, China
| | - Ting Ma
- Department of Transfusion Medicine, Shaanxi Provincial People's Hospital, 256 Youyi West Road, Xi'an, 710068, China
| | - Shu Su
- Clinical Research Management Office, The Second Affiliated Hospital of ChongQing Medical University, Chongqing, China
| | - Lin Wang
- AIM Lab, Faculty of IT, Monash University, Melbourne, VIC, Australia
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, China
| | - Xianwen Shang
- Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Zhuoting Zhu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, VIC, Australia
- Division of Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, VIC, Australia
| | - Yuhang Zhai
- Gies College of Business, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mingguang He
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, VIC, Australia
- Division of Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, VIC, Australia
| | - Zengbin Li
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, China
| | - Hanting Liu
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, China
| | - Christopher K Fairley
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Jiangcun Yang
- Department of Transfusion Medicine, Shaanxi Provincial People's Hospital, 256 Youyi West Road, Xi'an, 710068, China.
| | - Lei Zhang
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shaanxi, China.
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia.
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.
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23
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Ren X, Lei Y, Grebogi C, Baptista MS. The complementary contribution of each order topology into the synchronization of multi-order networks. CHAOS (WOODBURY, N.Y.) 2023; 33:111101. [PMID: 37909900 DOI: 10.1063/5.0177687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023]
Abstract
Higher-order interactions improve our capability to model real-world complex systems ranging from physics and neuroscience to economics and social sciences. There is great interest nowadays in understanding the contribution of higher-order terms to the collective behavior of the network. In this work, we investigate the stability of complete synchronization of complex networks with higher-order structures. We demonstrate that the synchronization level of a network composed of nodes interacting simultaneously via multiple orders is maintained regardless of the intensity of coupling strength across different orders. We articulate that lower-order and higher-order topologies work together complementarily to provide the optimal stable configuration, challenging previous conclusions that higher-order interactions promote the stability of synchronization. Furthermore, we find that simply adding higher-order interactions based on existing connections, as in simple complexes, does not have a significant impact on synchronization. The universal applicability of our work lies in the comprehensive analysis of different network topologies, including hypergraphs and simplicial complexes, and the utilization of appropriate rescaling to assess the impact of higher-order interactions on synchronization stability.
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Affiliation(s)
- Xiaomin Ren
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Youming Lei
- School of Mathematics and Statistics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Celso Grebogi
- Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Murilo S Baptista
- Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
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24
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Goździejewska AM, Kruk M. The response of zooplankton network indicators to winter water warming using shallow artificial reservoirs as model case study. Sci Rep 2023; 13:18002. [PMID: 37865664 PMCID: PMC10590368 DOI: 10.1038/s41598-023-45430-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/19/2023] [Indexed: 10/23/2023] Open
Abstract
To predict the most likely scenarios, the consequences of the rise in water surface temperature have been studied using various methods. We tested the hypothesis that winter water warming significantly alters the importance and nature of the relationships in zooplankton communities in shallow reservoirs. These relationships were investigated using network graph analysis for three thermal variants: warm winters (WW), moderate winters (MW) and cold winters (CW). The CW network was the most cohesive and was controlled by eutrophic Rotifera and Copepoda, with a corresponding number of positive and negative interspecific relationships. An increase in water temperature in winter led to a decrease in the centrality of MW and WW networks, and an increase in the importance of species that communicated with the highest number of species in the subnetworks. The WW network was the least cohesive, controlled by psammophilous and phytophilous rotifers, and littoral cladocerans. Adult copepods were not identified in the network and the importance of antagonistic relationships decreased, indicating that the WW network structure was weak and unstable. This study can serve as a model for generalisations of zooplankton community response to the disappearance of long winter periods of low temperatures, as predicted in global climate change projections.
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Affiliation(s)
- Anna Maria Goździejewska
- Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Oczapowskiego 5, 10-719, Olsztyn, Poland.
| | - Marek Kruk
- Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Słoneczna 54, 10-710, Olsztyn, Poland
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25
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Wang W, Ji D, Peng S, Loladze I, Harrison MT, Davies WJ, Smith P, Xia L, Wang B, Liu K, Zhu K, Zhang W, Ouyang L, Liu L, Gu J, Zhang H, Yang J, Wang F. Eco-physiology and environmental impacts of newly developed rice genotypes for improved yield and nitrogen use efficiency coordinately. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165294. [PMID: 37414171 DOI: 10.1016/j.scitotenv.2023.165294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/08/2023]
Abstract
Significant advancements have been made in understanding the genetic regulation of nitrogen use efficiency (NUE) and identifying crucial NUE genes in rice. However, the development of rice genotypes that simultaneously exhibit high yield and NUE has lagged behind these theoretical advancements. The grain yield, NUE, and greenhouse gas (GHG) emissions of newly-bred rice genotypes under reduced nitrogen application remain largely unknown. To address this knowledge gap, field experiments were conducted, involving 80 indica (14 to 19 rice genotypes each year in Wuxue, Hubei) and 12 japonica (8 to 12 rice genotypes each year in Yangzhou, Jiangsu). Yield, NUE, agronomy, and soil parameters were assessed, and climate data were recorded. The experiments aimed to assess genotypic variations in yield and NUE among these genotypes and to investigate the eco-physiological basis and environmental impacts of coordinating high yield and high NUE. The results showed significant variations in yield and NUE among the genotypes, with 47 genotypes classified as moderate-high yield with high NUE (MHY_HNUE). These genotypes demonstrated the higher yields and NUE levels, with 9.6 t ha-1, 54.4 kg kg-1, 108.1 kg kg-1, and 64 % for yield, NUE for grain and biomass production, and N harvest index, respectively. Nitrogen uptake and tissue concentration were key drivers of the relationship between yield and NUE, particularly N uptake at heading and N concentrations in both straw and grain at maturity. Increase in pre-anthesis temperature consistently lowered yield and NUE. Genotypes within the MHY_HNUE group exhibited higher methane emissions but lower nitrous oxide emissions compared to those in the low to middle yield and NUE group, resulting in a 12.8 % reduction in the yield-scaled greenhouse gas balance. In conclusion, prioritizing crop breeding efforts on yield and resource use efficiency, as well as developing genotypes resilient to high temperatures with lower GHGs, can mitigate planetary warming.
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Affiliation(s)
- Weilu Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Dongling Ji
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Shaobing Peng
- MARA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Irakli Loladze
- Bryan College of Health Sciences, Bryan Medical Center, Lincoln, NE 68506, USA
| | - Matthew Tom Harrison
- Tasmanian Institute of Agriculture, University of Tasmania, Newnham Drive, Launceston, Tasmania 7248, Australia
| | | | - Pete Smith
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Longlong Xia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bin Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ke Liu
- Tasmanian Institute of Agriculture, University of Tasmania, Newnham Drive, Launceston, Tasmania 7248, Australia
| | - Kuanyu Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wen Zhang
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100071, China
| | - Linhan Ouyang
- College of Economics and Management, Department of Management Science and Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Lijun Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Junfei Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jianchang Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Fei Wang
- MARA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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26
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Pasquier C, Guerlais V, Pallez D, Rapetti-Mauss R, Soriani O. A network embedding approach to identify active modules in biological interaction networks. Life Sci Alliance 2023; 6:e202201550. [PMID: 37339804 PMCID: PMC10282331 DOI: 10.26508/lsa.202201550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/22/2023] Open
Abstract
The identification of condition-specific gene sets from transcriptomic experiments is important to reveal regulatory and signaling mechanisms associated with a given cellular response. Statistical methods of differential expression analysis, designed to assess individual gene variations, have trouble highlighting modules of small varying genes whose interaction is essential to characterize phenotypic changes. To identify these highly informative gene modules, several methods have been proposed in recent years, but they have many limitations that make them of little use to biologists. Here, we propose an efficient method for identifying these active modules that operates on a data embedding combining gene expressions and interaction data. Applications carried out on real datasets show that our method can identify new groups of genes of high interest corresponding to functions not revealed by traditional approaches. Software is available at https://github.com/claudepasquier/amine.
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Affiliation(s)
- Claude Pasquier
- Laboratoire d'Informatique, Signaux et Systèmes de Sophia-Antipolis, I3S - UMR7271 - UNS CNRS, Les Algorithmes - bât. Euclide B, Sophia Antipolis, France
| | - Vincent Guerlais
- Laboratoire d'Informatique, Signaux et Systèmes de Sophia-Antipolis, I3S - UMR7271 - UNS CNRS, Les Algorithmes - bât. Euclide B, Sophia Antipolis, France
| | - Denis Pallez
- Laboratoire d'Informatique, Signaux et Systèmes de Sophia-Antipolis, I3S - UMR7271 - UNS CNRS, Les Algorithmes - bât. Euclide B, Sophia Antipolis, France
| | - Raphaël Rapetti-Mauss
- iBV - Institut de Biologie Valrose, Université Nice Sophia Antipolis, Faculté des Sciences, Parc Valrose, Nice cedex 2, France
| | - Olivier Soriani
- iBV - Institut de Biologie Valrose, Université Nice Sophia Antipolis, Faculté des Sciences, Parc Valrose, Nice cedex 2, France
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27
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Marino A, Sinaimeri B, Tronci E, Calamoneri T. STARGATE-X: a Python package for statistical analysis on the REACTOME network. J Integr Bioinform 2023; 20:jib-2022-0029. [PMID: 37732505 PMCID: PMC10757075 DOI: 10.1515/jib-2022-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/24/2023] [Indexed: 09/22/2023] Open
Abstract
Many important aspects of biological knowledge at the molecular level can be represented by pathways. Through their analysis, we gain mechanistic insights and interpret lists of interesting genes from experiments (usually omics and functional genomic experiments). As a result, pathways play a central role in the development of bioinformatics methods and tools for computing predictions from known molecular-level mechanisms. Qualitative as well as quantitative knowledge about pathways can be effectively represented through biochemical networks linking the biochemical reactions and the compounds (e.g., proteins) occurring in the considered pathways. So, repositories providing biochemical networks for known pathways play a central role in bioinformatics and in systems biology. Here we focus on Reactome, a free, comprehensive, and widely used repository for biochemical networks and pathways. In this paper, we: (1) introduce a tool StARGate-X (STatistical Analysis of the Reactome multi-GrAph Through nEtworkX) to carry out an automated analysis of the connectivity properties of Reactome biochemical reaction network and of its biological hierarchy (i.e., cell compartments, namely, the closed parts within the cytosol, usually surrounded by a membrane); the code is freely available at https://github.com/marinoandrea/stargate-x; (2) show the effectiveness of our tool by providing an analysis of the Reactome network, in terms of centrality measures, with respect to in- and out-degree. As an example of usage of StARGate-X, we provide a detailed automated analysis of the Reactome network, in terms of centrality measures. We focus both on the subgraphs induced by single compartments and on the graph whose nodes are the strongly connected components. To the best of our knowledge, this is the first freely available tool that enables automatic analysis of the large biochemical network within Reactome through easy-to-use APIs (Application Programming Interfaces).
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Affiliation(s)
- Andrea Marino
- Computer Science Department, Sapienza University of Rome, Rome, Italy
| | | | - Enrico Tronci
- Computer Science Department, Sapienza University of Rome, Rome, Italy
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28
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Pakulnicka J, Kruk M. Regional differences in water beetle communities networks settling in dystrophic lakes in northern Poland. Sci Rep 2023; 13:12699. [PMID: 37543705 PMCID: PMC10404283 DOI: 10.1038/s41598-023-39689-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 07/29/2023] [Indexed: 08/07/2023] Open
Abstract
The relationships between the species that form the networks in small dystrophic lakes remain poorly recognised. To investigate and better understand the functioning of beetle communities in different ecosystems, we created three network models that we subjected to graph network analysis. This approach displays correlation-based networks of connections (edges) between objects (nodes) by evaluating the features of the whole network and the attributes of nodes and edges in the context of their roles, expressed by centrality metrics. We used this method to determine the importance of specific species in the networks and the interspecific relationships. Our analyses are based on faunal material collected from 25 dystrophic lakes in three regions of northern Poland. We found a total of 104 species representing different ecological elements and functional trophic groups. We have shown that the network of relationships between the biomass of species differs considerably in the three study regions. The Kashubian Lakeland had the highest cohesion and density, while the network in the Suwalki Lakeland was the thinnest and most heterogeneous, which might be related to the fractal structure and the degree of development of the studied lakes. Small-bodied predators that congregated in different clusters with species with similar ecological preferences dominated all networks. We found the highest correlations in the Masurian Lakeland, where we obtained the highest centralisation of the network. Small tyrphophiles typically occupied the central places in the network, while the periphery of the network consisted of clusters with different habitat preferences, including large predators. The species that were most important for network cohesion and density were mainly tyrphophilous species, such as Anacaena lutescens, Hygrotus decoratus, Enochrus melanocephalus and Hydroporus neglectus. The values of attributes determining the role of species in community networks were influenced by both biotic and environmental factors.
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Affiliation(s)
- Joanna Pakulnicka
- Department of Ecology and Environmental Protection, University of Warmia and Mazury in Olsztyn, Lodzki sq. 3, 10-727, Olsztyn, Poland.
| | - Marek Kruk
- Department of Mathematical Modelling and Applied Informatics, University of Warmia and Mazury in Olsztyn, Sloneczna 54, 10-719, Olsztyn, Poland
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Barratt LJ, He Z, Fellgett A, Wang L, Mason SM, Bancroft I, Harper AL. Co-expression network analysis of diverse wheat landraces reveals markers of early thermotolerance and a candidate master regulator of thermotolerance genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:614-626. [PMID: 37077043 PMCID: PMC10953029 DOI: 10.1111/tpj.16248] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Triticum aestivum L. (bread wheat) is a crop relied upon by billions of people around the world, as a major source of both income and calories. Rising global temperatures, however, pose a genuine threat to the livelihood of these people, as wheat growth and yields are extremely vulnerable to damage by heat stress. Here we present the YoGI wheat landrace panel, comprising 342 accessions that show remarkable phenotypic and genetic diversity thanks to their adaptation to different climates. We quantified the abundance of 110 790 transcripts from the panel and used these data to conduct weighted co-expression network analysis and to identify hub genes in modules associated with abiotic stress tolerance. We found that the expression of three hub genes, all heat-shock proteins (HSPs), were significantly correlated with early thermotolerance in a validation panel of landraces. These hub genes belong to the same module, with one (TraesCS4D01G207500.1) being a candidate master-regulator potentially controlling the expression of the other two hub genes, as well as a suite of other HSPs and heat-stress transcription factors (HSFs). In this work, therefore, we identify three validated hub genes, the expression of which can serve as markers of thermotolerance during early development, and suggest that TraesCS4D01G207500.1 is a potential master regulator of HSP and HSF expression - presenting the YoGI landrace panel as an invaluable tool for breeders wishing to determine and introduce novel alleles into modern varieties, for the production of climate-resilient crops.
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Affiliation(s)
- Liam J. Barratt
- Department of Biology, Centre for Novel Agricultural Products (CNAP)University of YorkWentworth WayYO10 5DDUK
| | - Zhesi He
- Department of Biology, Centre for Novel Agricultural Products (CNAP)University of YorkWentworth WayYO10 5DDUK
| | - Alison Fellgett
- Department of Biology, Centre for Novel Agricultural Products (CNAP)University of YorkWentworth WayYO10 5DDUK
| | - Lihong Wang
- Department of Biology, Centre for Novel Agricultural Products (CNAP)University of YorkWentworth WayYO10 5DDUK
| | - Simon McQueen Mason
- Department of Biology, Centre for Novel Agricultural Products (CNAP)University of YorkWentworth WayYO10 5DDUK
| | - Ian Bancroft
- Department of Biology, Centre for Novel Agricultural Products (CNAP)University of YorkWentworth WayYO10 5DDUK
| | - Andrea L. Harper
- Department of Biology, Centre for Novel Agricultural Products (CNAP)University of YorkWentworth WayYO10 5DDUK
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30
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Lee YT, Chen SJ. Graph theory applications in congenital heart disease. Sci Rep 2023; 13:11135. [PMID: 37429950 DOI: 10.1038/s41598-023-38233-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023] Open
Abstract
Graph theory can be used to address problems with complex network structures. Congenital heart diseases (CHDs) involve complex abnormal connections between chambers, vessels, and organs. We proposed a new method to represent CHDs based on graph theory, wherein vertices were defined as the spaces through which blood flows and edges were defined by the blood flow between the spaces and direction of the blood flow. The CHDs of tetralogy of Fallot (TOF) and transposition of the great arteries (TGA) were selected as examples for constructing directed graphs and binary adjacency matrices. Patients with totally repaired TOF, surgically corrected d-TGA, and Fontan circulation undergoing four-dimensional (4D) flow magnetic resonance imaging (MRI) were included as examples for constructing the weighted adjacency matrices. The directed graphs and binary adjacency matrices of the normal heart, extreme TOF undergoing a right modified Blalock-Taussig shunt, and d-TGA with a ventricular septal defect were constructed. The weighted adjacency matrix of totally repaired TOF was constructed using the peak velocities obtained from 4D flow MRI. The developed method is promising for representing CHDs and may be helpful in developing artificial intelligence and conducting future research on CHD.
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Affiliation(s)
- Yao-Ting Lee
- Department of Medical Imaging, National Taiwan University Hospital and Children Hospital, National Taiwan University, 7 Chung-Shan South Road, Taipei, 10002, Taiwan
| | - Shyh-Jye Chen
- Department of Medical Imaging, National Taiwan University Hospital and Children Hospital, National Taiwan University, 7 Chung-Shan South Road, Taipei, 10002, Taiwan.
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31
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Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DB, Ma’ayan A. Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Res 2023; 51:W168-W179. [PMID: 37166973 PMCID: PMC10320098 DOI: 10.1093/nar/gkad393] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/23/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023] Open
Abstract
Gene and protein set enrichment analysis is a critical step in the analysis of data collected from omics experiments. Enrichr is a popular gene set enrichment analysis web-server search engine that contains hundreds of thousands of annotated gene sets. While Enrichr has been useful in providing enrichment analysis with many gene set libraries from different categories, integrating enrichment results across libraries and domains of knowledge can further hypothesis generation. To this end, Enrichr-KG is a knowledge graph database and a web-server application that combines selected gene set libraries from Enrichr for integrative enrichment analysis and visualization. The enrichment results are presented as subgraphs made of nodes and links that connect genes to their enriched terms. In addition, users of Enrichr-KG can add gene-gene links, as well as predicted genes to the subgraphs. This graphical representation of cross-library results with enriched and predicted genes can illuminate hidden associations between genes and annotated enriched terms from across datasets and resources. Enrichr-KG currently serves 26 gene set libraries from different categories that include transcription, pathways, ontologies, diseases/drugs, and cell types. To demonstrate the utility of Enrichr-KG we provide several case studies. Enrichr-KG is freely available at: https://maayanlab.cloud/enrichr-kg.
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Affiliation(s)
- John Erol Evangelista
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Zhuorui Xie
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Nhi Nguyen
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, NY, NY, USA
| | - Avi Ma’ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, NY, NY, USA
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32
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Fan D, Schwinghamer T, Liu S, Xia O, Ge C, Chen Q, Smith DL. Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes. FRONTIERS IN PLANT SCIENCE 2023; 14:1176648. [PMID: 37404529 PMCID: PMC10316030 DOI: 10.3389/fpls.2023.1176648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/24/2023] [Indexed: 07/06/2023]
Abstract
Introduction The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf). Methods In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes. Results and discussion Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.
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Affiliation(s)
- Di Fan
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Timothy Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shuaitong Liu
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Ouyuan Xia
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Chunmei Ge
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Qun Chen
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Donald L. Smith
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
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Inge Schytz Andersen-Civil A, Anjan Sawale R, Claude Vanwalleghem G. Zebrafish (Danio rerio) as a translational model for neuro-immune interactions in the enteric nervous system in autism spectrum disorders. Brain Behav Immun 2023:S0889-1591(23)00142-3. [PMID: 37301234 DOI: 10.1016/j.bbi.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/28/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023] Open
Abstract
Autism spectrum disorders (ASD) affect about 1% of the population and are strongly associated with gastrointestinal diseases creating shortcomings in quality of life. Multiple factors contribute to the development of ASD and although neurodevelopmental deficits are central, the pathogenesis of the condition is complex and the high prevalence of intestinal disorders is poorly understood. In agreement with the prominent research establishing clear bidirectional interactions between the gut and the brain, several studies have made it evident that such a relation also exists in ASD. Thus, dysregulation of the gut microbiota and gut barrier integrity may play an important role in ASD. However, only limited research has investigated how the enteric nervous system (ENS) and intestinal mucosal immune factors may impact on the development of ASD-related intestinal disorders. This review focuses on the mechanistic studies that elucidate the regulation and interactions between enteric immune cells, residing gut microbiota and the ENS in models of ASD. Especially the multifaceted properties and applicability of zebrafish (Danio rerio) for the study of ASD pathogenesis are assessed in comparison to studies conducted in rodent models and humans. Advances in molecular techniques and in vivo imaging, combined with genetic manipulation and generation of germ-free animals in a controlled environment, appear to make zebrafish an underestimated model of choice for the study of ASD. Finally, we establish the research gaps that remain to be explored to further our understanding of the complexity of ASD pathogenesis and associated mechanisms that may lead to intestinal disorders.
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Affiliation(s)
- Audrey Inge Schytz Andersen-Civil
- Department of Molecular Biology and Genetics, Universitetsbyen 81, 8000 Aarhus C, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark.
| | - Rajlakshmi Anjan Sawale
- Department of Molecular Biology and Genetics, Universitetsbyen 81, 8000 Aarhus C, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Gilles Claude Vanwalleghem
- Department of Molecular Biology and Genetics, Universitetsbyen 81, 8000 Aarhus C, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
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34
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Baker CM, Gong Y. Identifying properties of pattern completion neurons in a computational model of the visual cortex. PLoS Comput Biol 2023; 19:e1011167. [PMID: 37279242 DOI: 10.1371/journal.pcbi.1011167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
Neural ensembles are found throughout the brain and are believed to underlie diverse cognitive functions including memory and perception. Methods to activate ensembles precisely, reliably, and quickly are needed to further study the ensembles' role in cognitive processes. Previous work has found that ensembles in layer 2/3 of the visual cortex (V1) exhibited pattern completion properties: ensembles containing tens of neurons were activated by stimulation of just two neurons. However, methods that identify pattern completion neurons are underdeveloped. In this study, we optimized the selection of pattern completion neurons in simulated ensembles. We developed a computational model that replicated the connectivity patterns and electrophysiological properties of layer 2/3 of mouse V1. We identified ensembles of excitatory model neurons using K-means clustering. We then stimulated pairs of neurons in identified ensembles while tracking the activity of the entire ensemble. Our analysis of ensemble activity quantified a neuron pair's power to activate an ensemble using a novel metric called pattern completion capability (PCC) based on the mean pre-stimulation voltage across the ensemble. We found that PCC was directly correlated with multiple graph theory parameters, such as degree and closeness centrality. To improve selection of pattern completion neurons in vivo, we computed a novel latency metric that was correlated with PCC and could potentially be estimated from modern physiological recordings. Lastly, we found that stimulation of five neurons could reliably activate ensembles. These findings can help researchers identify pattern completion neurons to stimulate in vivo during behavioral studies to control ensemble activation.
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Affiliation(s)
- Casey M Baker
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Yiyang Gong
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Department of Neurobiology, Duke University, Durham, North Carolina, United States of America
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35
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Norkaew C, Subkorn P, Chatupheeraphat C, Roytrakul S, Tanyong D. Pinostrobin, a fingerroot compound, regulates miR-181b-5p and induces acute leukemic cell apoptosis. Sci Rep 2023; 13:8084. [PMID: 37208425 DOI: 10.1038/s41598-023-35193-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/14/2023] [Indexed: 05/21/2023] Open
Abstract
Pinostrobin (PN) is the most abundant flavonoid found in fingerroot. Although the anti-leukemic properties of PN have been reported, its mechanisms are still unclear. MicroRNAs (miRNAs) are small RNA molecules that function in posttranscriptional silencing and are increasingly being used in cancer therapy. The aims of this study were to investigate the effects of PN on proliferation inhibition and induction of apoptosis, as well as the involvement of miRNAs in PN-mediated apoptosis in acute leukemia. The results showed that PN reduced cell viability and induced apoptosis in acute leukemia cells via both intrinsic and extrinsic pathways. A bioinformatics approach and Protein-Protein Interaction (PPI) network analysis revealed that ataxia-telangiectasia mutated kinase (ATM), one of the p53 activators that responds to DNA damage-induced apoptosis, is a crucial target of PN. Four prediction tools were used to predict ATM-regulated miRNAs; miR-181b-5p was the most likely candidate. The reduction in miR-181b-5 after PN treatment was found to trigger ATM, resulting in cellular apoptosis. Therefore, PN could be developed as a drug for acute leukemia; in addition, miR-181b-5p and ATM may be promising therapeutic targets.
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Affiliation(s)
- Chosita Norkaew
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Paweena Subkorn
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Chawalit Chatupheeraphat
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology for Development Agency, Pathum Thani, 12120, Thailand
| | - Dalina Tanyong
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, 73170, Thailand.
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36
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Kim KS, Moon SW, Moon MH, Hyun KY, Kim SJ, Kim YK, Kim KY, Jekarl DW, Oh EJ, Kim Y. Metabolic profiles of lung adenocarcinoma via peripheral blood and diagnostic model construction. Sci Rep 2023; 13:7304. [PMID: 37147444 PMCID: PMC10163250 DOI: 10.1038/s41598-023-34575-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/03/2023] [Indexed: 05/07/2023] Open
Abstract
The metabolic profile of cancerous cells is shifted to meet the cellular demand required for proliferation and growth. Here we show the features of cancer metabolic profiles using peripheral blood of healthy control subjects (n = 78) and lung adenocarcinoma (LUAD) patients (n = 64). Among 121 detected metabolites, diagnosis of LUAD is based on arginine, lysophosphatidylcholine-acyl (Lyso.PC.a) C16:0, and PC-diacyl (PC.aa) C38:3. Network analysis revealed that network heterogeneity, diameter, and shortest path were decreased in LUAD. On the contrary, these parameters were increased in advanced-stage compared to early-stage LUAD. Clustering coefficient, network density, and average degree were increased in LUAD compared to the healthy control, whereas these topologic parameters were decreased in advanced-stage compared to early-stage LUAD. Public LUAD data verified that the genes encoding enzymes for arginine (NOS, ARG, AZIN) and for Lyso.PC and PC (CHK, PCYT, LPCAT) were related with overall survival. Further studies are required to verify these results with larger samples and other histologic types of lung cancer.
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Affiliation(s)
- Kyung Soo Kim
- Department of Thoracic and Cardiovascular Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seok Whan Moon
- Department of Thoracic and Cardiovascular Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Mi Hyung Moon
- Department of Thoracic and Cardiovascular Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kwan Yong Hyun
- Department of Thoracic and Cardiovascular Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Joon Kim
- Department of Pulmonology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Young Koon Kim
- Department of Pulmonology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kwang Youl Kim
- Department of Clinical Pharmacology, Inha University Hospital, Inha University, 27 Inhang-ro, Jung-gu, Incheon, 22332, Republic of Korea.
| | - Dong Wook Jekarl
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-gu, Seoul, 06591, Republic of Korea.
- Research and Development Institute for In Vitro Diagnostic Medical Devices, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Eun-Jee Oh
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Research and Development Institute for In Vitro Diagnostic Medical Devices, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-gu, Seoul, 06591, Republic of Korea
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37
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Ahmed F, Samantasinghar A, Manzoor Soomro A, Kim S, Hyun Choi K. A systematic review of computational approaches to understand cancer biology for informed drug repurposing. J Biomed Inform 2023; 142:104373. [PMID: 37120047 DOI: 10.1016/j.jbi.2023.104373] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
Cancer is the second leading cause of death globally, trailing only heart disease. In the United States alone, 1.9 million new cancer cases and 609,360 deaths were recorded for 2022. Unfortunately, the success rate for new cancer drug development remains less than 10%, making the disease particularly challenging. This low success rate is largely attributed to the complex and poorly understood nature of cancer etiology. Therefore, it is critical to find alternative approaches to understanding cancer biology and developing effective treatments. One such approach is drug repurposing, which offers a shorter drug development timeline and lower costs while increasing the likelihood of success. In this review, we provide a comprehensive analysis of computational approaches for understanding cancer biology, including systems biology, multi-omics, and pathway analysis. Additionally, we examine the use of these methods for drug repurposing in cancer, including the databases and tools that are used for cancer research. Finally, we present case studies of drug repurposing, discussing their limitations and offering recommendations for future research in this area.
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Affiliation(s)
- Faheem Ahmed
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea
| | | | | | - Sejong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Kyung Hyun Choi
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea.
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38
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Baron C, Cherkaoui S, Therrien-Laperriere S, Ilboudo Y, Poujol R, Mehanna P, Garrett ME, Telen MJ, Ashley-Koch AE, Bartolucci P, Rioux JD, Lettre G, Des Rosiers C, Ruiz M, Hussin JG. Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533869. [PMID: 36993181 PMCID: PMC10055409 DOI: 10.1101/2023.03.22.533869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Studies combining metabolomics and genetics, known as metabolite genome-wide association studies (mGWAS), have provided valuable insights into our understanding of the genetic control of metabolite levels. However, the biological interpretation of these associations remains challenging due to a lack of existing tools to annotate mGWAS gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we computed the shortest reactional distance (SRD) based on the curated knowledge of the KEGG database to explore its utility in enhancing the biological interpretation of results from three independent mGWAS, including a case study on sickle cell disease patients. Results show that, in reported mGWAS pairs, there is an excess of small SRD values and that SRD values and p-values significantly correlate, even beyond the standard conservative thresholds. The added-value of SRD annotation is shown for identification of potential false negative hits, exemplified by the finding of gene-metabolite associations with SRD ≤1 that did not reach standard genome-wide significance cut-off. The wider use of this statistic as an mGWAS annotation would prevent the exclusion of biologically relevant associations and can also identify errors or gaps in current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs that can be used to integrate statistical evidence to biological networks.
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Affiliation(s)
- Cantin Baron
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Québec, Canada
- Montreal Heart Institute, Québec, Canada
| | - Sarah Cherkaoui
- Montreal Heart Institute, Québec, Canada
- Division of Oncology and Children’s Research Center, University Children’s Hospital Zurich, University of Zurich, Switzerland
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France
| | | | - Yann Ilboudo
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Québec, Canada
- Montreal Heart Institute, Québec, Canada
| | | | | | - Melanie E. Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Marilyn J. Telen
- Division of Hematology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Pablo Bartolucci
- Université Paris Est Créteil, Hôpitaux Universitaires Henri Mondor, APHP, Sickle cell referral center – UMGGR, Créteil, France
- Université Paris Est Créteil, IMRB, Laboratory of excellence LABEX, Créteil, France
| | - John D. Rioux
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Québec, Canada
- Montreal Heart Institute, Québec, Canada
- Département de Médecine, Université de Montréal, Québec, Canada
| | - Guillaume Lettre
- Montreal Heart Institute, Québec, Canada
- Département de Médecine, Université de Montréal, Québec, Canada
| | - Christine Des Rosiers
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Québec, Canada
- Montreal Heart Institute, Québec, Canada
- Département de Nutrition, Université de Montréal, Québec, Canada
| | - Matthieu Ruiz
- Montreal Heart Institute, Québec, Canada
- Département de Nutrition, Université de Montréal, Québec, Canada
| | - Julie G. Hussin
- Montreal Heart Institute, Québec, Canada
- Département de Médecine, Université de Montréal, Québec, Canada
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39
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Flores-Díaz A, Escoto-Sandoval C, Cervantes-Hernández F, Ordaz-Ortiz JJ, Hayano-Kanashiro C, Reyes-Valdés H, Garcés-Claver A, Ochoa-Alejo N, Martínez O. Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1148. [PMID: 36904008 PMCID: PMC10005043 DOI: 10.3390/plants12051148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Gene co-expression networks are powerful tools to understand functional interactions between genes. However, large co-expression networks are difficult to interpret and do not guarantee that the relations found will be true for different genotypes. Statistically verified time expression profiles give information about significant changes in expressions through time, and genes with highly correlated time expression profiles, which are annotated in the same biological process, are likely to be functionally connected. A method to obtain robust networks of functionally related genes will be useful to understand the complexity of the transcriptome, leading to biologically relevant insights. We present an algorithm to construct gene functional networks for genes annotated in a given biological process or other aspects of interest. We assume that there are genome-wide time expression profiles for a set of representative genotypes of the species of interest. The method is based on the correlation of time expression profiles, bound by a set of thresholds that assure both, a given false discovery rate, and the discard of correlation outliers. The novelty of the method consists in that a gene expression relation must be repeatedly found in a given set of independent genotypes to be considered valid. This automatically discards relations particular to specific genotypes, assuring a network robustness, which can be set a priori. Additionally, we present an algorithm to find transcription factors candidates for regulating hub genes within a network. The algorithms are demonstrated with data from a large experiment studying gene expression during the development of the fruit in a diverse set of chili pepper genotypes. The algorithm is implemented and demonstrated in a new version of the publicly available R package "Salsa" (version 1.0).
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Affiliation(s)
- Alan Flores-Díaz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Christian Escoto-Sandoval
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Felipe Cervantes-Hernández
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - José J. Ordaz-Ortiz
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Corina Hayano-Kanashiro
- Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo 83000, Mexico
| | - Humberto Reyes-Valdés
- Department of Plant Breeding, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico
| | - Ana Garcés-Claver
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain
| | - Neftalí Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
| | - Octavio Martínez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
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Khalafiyan A, Emadi-Baygi M, Wolfien M, Salehzadeh-Yazdi A, Nikpour P. Construction of a three-component regulatory network of transcribed ultraconserved regions for the identification of prognostic biomarkers in gastric cancer. J Cell Biochem 2023; 124:396-408. [PMID: 36748954 DOI: 10.1002/jcb.30373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Altered expression and functional roles of the transcribed ultraconserved regions (T-UCRs), as genomic sequences with 100% conservation between the genomes of human, mouse, and rat, in the pathophysiology of neoplasms has already been investigated. Nevertheless, the relevance of the functions for T-UCRs in gastric cancer (GC) is still the subject of inquiry. In the current study, we first used a genome-wide profiling approach to analyze the expression of T-UCRs in GC patients. Then, we constructed a three-component regulatory network and investigated potential diagnostic and prognostic values of the T-UCRs. The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) dataset was used as a resource for the RNA-sequencing data. FeatureCounts was utilized to quantify the number of reads mapped to each T-UCR. Differential expression analysis was then conducted using DESeq2. In the following, interactions between T-UCRs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were combined into a three-component network. Enrichment analyses were performed and a protein-protein interaction (PPI) network was constructed. The R Survival package was utilized to identify survival-related significantly differentially expressed T-UCRs (DET-UCRs). Using an in-house cohort of GC tissues, expression of two DET-UCRs was furthermore experimentally verified. Our results showed that several T-UCRs were dysregulated in TCGA-STAD tumoral samples compared to nontumoral counterparts. The three-component network was constructed which composed of DET-UCRs, miRNAs, and mRNAs nodes. Functional enrichment and PPI network analyses revealed important enriched signaling pathways and gene ontologies such as "pathway in cancer" and regulation of cell proliferation and apoptosis. Five T-UCRs were significantly correlated with the overall survival of GC patients. While no expression of uc.232 was observed in our in-house cohort of GC tissues, uc.343 showed an increased expression, although not statistically significant, in gastric tumoral tissues. The constructed three-component regulatory network of T-UCRs in GC presents a comprehensive understanding of the underlying gene expression regulation processes involved in tumor development and can serve as a basis to investigate potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Anis Khalafiyan
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Markus Wolfien
- Department of System Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Center for Medical Informatics, Dresden, Germany
| | - Ali Salehzadeh-Yazdi
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Parvaneh Nikpour
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Geoffrey A S B, Madaj R, Valluri PP. QPoweredCompound2DeNovoDrugPropMax - a novel programmatic tool incorporating deep learning and in silico methods for automated in silico bio-activity discovery for any compound of interest. J Biomol Struct Dyn 2023; 41:1790-1797. [PMID: 35007471 DOI: 10.1080/07391102.2021.2024450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Network data is composed of nodes and edges. Successful application of machine learning/deep learning algorithms on network data to make node classification and link prediction have been shown in the area of social networks through which highly customized suggestions are offered to social network users. Similarly one can attempt the use of machine learning/deep learning algorithms on biological network data to generate predictions of scientific usefulness. In the presented work, compound-drug target interaction network data set from bindingDB has been used to train deep learning neural network and a multi class classification has been implemented to classify PubChem compound queried by the user into class labels of PBD IDs. This way target interaction prediction for PubChem compounds is carried out using deep learning. The user is required to input the PubChem Compound ID (CID) of the compound the user wishes to gain information about its predicted biological activity and the tool outputs the RCSB PDB IDs of the predicted drug target interaction for the input CID. Further the tool also optimizes the compound of interest of the user toward drug likeness properties through a deep learning based structure optimization protocol. The tool also incorporates a feature to perform automated In Silico modelling to find the interaction between the compounds and the predicted drug targets to uncover their protein-ligand interaction profiles. The program is hosted, supported and maintained at the following GitHub repository. https://github.com/bengeof/Compound2DeNovoDrugPropMax. Anticipating the use of quantum computing and quantum machine learning in drug discovery we use the Penny-lane interface to quantum hardware to turn classical Keras layers used in our machine/deep learning models into a quantum layer and introduce quantum layers into classical models to produce a quantum-classical machine/deep learning hybrid model of our tool and the code corresponding to the same is provided below. https://github.com/bengeof/QPoweredCompound2DeNovoDrugPropMax.HIGHLIGHTSDeep learning based network pharmacology approach to predict the bio-activity of compounds.Further optimization of the compound toward drug like properties using deep learning techniques.Automated in silico modeling and interaction profiling of deep learning predicted target protein-ligand interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ben Geoffrey A S
- Department of Physics, Madras Christian College affiliated to the University of Madras, Chennai, India
| | - Rafal Madaj
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Pavan Preetham Valluri
- Applied mathematics and computational science, PSG College of Technology, Coimbatore, India
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Lucas M, Morris A, Townsend-Teague A, Tichit L, Habermann B, Barrat A. Inferring cell cycle phases from a partially temporal network of protein interactions. CELL REPORTS METHODS 2023; 3:100397. [PMID: 36936083 PMCID: PMC10014271 DOI: 10.1016/j.crmeth.2023.100397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
The temporal organization of biological systems is key for understanding them, but current methods for identifying this organization are often ad hoc and require prior knowledge. We present Phasik, a method that automatically identifies this multiscale organization by combining time series data (protein or gene expression) and interaction data (protein-protein interaction network). Phasik builds a (partially) temporal network and uses clustering to infer temporal phases. We demonstrate the method's effectiveness by recovering well-known phases and sub-phases of the cell cycle of budding yeast and phase arrests of mutants. We also show its general applicability using temporal gene expression data from circadian rhythms in wild-type and mutant mouse models. We systematically test Phasik's robustness and investigate the effect of having only partial temporal information. As time-resolved, multiomics datasets become more common, this method will allow the study of temporal regulation in lesser-known biological contexts, such as development, metabolism, and disease.
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Affiliation(s)
- Maxime Lucas
- Aix Marseille University, CNRS, I2M UMR 7373, Turing Center for Living Systems, Marseille, France
- Aix Marseille University, CNRS, IBDM UMR 7288, Turing Center for Living Systems, Marseille, France
- Aix Marseille University, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
| | | | | | - Laurent Tichit
- Aix Marseille University, CNRS, I2M UMR 7373, Turing Center for Living Systems, Marseille, France
| | - Bianca Habermann
- Aix Marseille University, CNRS, IBDM UMR 7288, Turing Center for Living Systems, Marseille, France
| | - Alain Barrat
- Aix Marseille University, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
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Zelenkovski K, Sandev T, Metzler R, Kocarev L, Basnarkov L. Random Walks on Networks with Centrality-Based Stochastic Resetting. ENTROPY (BASEL, SWITZERLAND) 2023; 25:293. [PMID: 36832659 PMCID: PMC9955709 DOI: 10.3390/e25020293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
We introduce a refined way to diffusely explore complex networks with stochastic resetting where the resetting site is derived from node centrality measures. This approach differs from previous ones, since it not only allows the random walker with a certain probability to jump from the current node to a deliberately chosen resetting node, rather it enables the walker to jump to the node that can reach all other nodes faster. Following this strategy, we consider the resetting site to be the geometric center, the node that minimizes the average travel time to all the other nodes. Using the established Markov chain theory, we calculate the Global Mean First Passage Time (GMFPT) to determine the search performance of the random walk with resetting for different resetting node candidates individually. Furthermore, we compare which nodes are better resetting node sites by comparing the GMFPT for each node. We study this approach for different topologies of generic and real-life networks. We show that, for directed networks extracted for real-life relationships, this centrality focused resetting can improve the search to a greater extent than for the generated undirected networks. This resetting to the center advocated here can minimize the average travel time to all other nodes in real networks as well. We also present a relationship between the longest shortest path (the diameter), the average node degree and the GMFPT when the starting node is the center. We show that, for undirected scale-free networks, stochastic resetting is effective only for networks that are extremely sparse with tree-like structures as they have larger diameters and smaller average node degrees. For directed networks, the resetting is beneficial even for networks that have loops. The numerical results are confirmed by analytic solutions. Our study demonstrates that the proposed random walk approach with resetting based on centrality measures reduces the memoryless search time for targets in the examined network topologies.
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Affiliation(s)
- Kiril Zelenkovski
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
| | - Trifce Sandev
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
- Institute of Physics, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, Arhimedova 3, 1000 Skopje, Macedonia
- Institute of Physics & Astronomy, University of Potsdam, D-14776 Potsdam, Germany
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, D-14776 Potsdam, Germany
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Ljupco Kocarev
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
- Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University, 1000 Skopje, Macedonia
| | - Lasko Basnarkov
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
- Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University, 1000 Skopje, Macedonia
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Characterization of the Gut Microbiota in Urban Thai Individuals Reveals Enterotype-Specific Signature. Microorganisms 2023; 11:microorganisms11010136. [PMID: 36677429 PMCID: PMC9866083 DOI: 10.3390/microorganisms11010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Gut microbiota play vital roles in human health, utilizing indigestible nutrients, producing essential substances, regulating the immune system, and inhibiting pathogen growth. Gut microbial profiles are dependent on populations, geographical locations, and long-term dietary patterns resulting in individual uniqueness. Gut microbiota can be classified into enterotypes based on their patterns. Understanding gut enterotype enables us to interpret the capability in macronutrient digestion, essential substance production, and microbial co-occurrence. However, there is still no detailed characterization of gut microbiota enterotype in urban Thai people. In this study, we characterized the gut microbiota of urban Thai individuals by amplicon sequencing and classified their profiles into enterotypes, including Prevotella (EnP) and Bacteroides (EnB) enterotypes. Enterotypes were associated with lifestyle, dietary habits, bacterial diversity, differential taxa, and microbial pathways. Microbe-microbe interactions have been studied via co-occurrence networks. EnP had lower α-diversities than those in EnB. A correlation analysis revealed that the Prevotella genus, the predominant taxa of EnP, has a negative correlation with α-diversities. Microbial function enrichment analysis revealed that the biosynthesis pathways of B vitamins and fatty acids were significantly enriched in EnP and EnB, respectively. Interestingly, Ruminococcaceae, resistant starch degraders, were the hubs of both enterotypes, and strongly correlated with microbial diversity, suggesting that traditional Thai food, consisting of rice and vegetables, might be the important drivers contributing to the gut microbiota uniqueness in urban Thai individuals. Overall findings revealed the biological uniqueness of gut enterotype in urban Thai people, which will be advantageous for developing gut microbiome-based diagnostic tools.
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Manipur I, Giordano M, Piccirillo M, Parashuraman S, Maddalena L. Community Detection in Protein-Protein Interaction Networks and Applications. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:217-237. [PMID: 34951849 DOI: 10.1109/tcbb.2021.3138142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The ability to identify and characterize not only the protein-protein interactions but also their internal modular organization through network analysis is fundamental for understanding the mechanisms of biological processes at the molecular level. Indeed, the detection of the network communities can enhance our understanding of the molecular basis of disease pathology, and promote drug discovery and disease treatment in personalized medicine. This work gives an overview of recent computational methods for the detection of protein complexes and functional modules in protein-protein interaction networks, also providing a focus on some of its applications. We propose a systematic reformulation of frequently adopted taxonomies for these methods, also proposing new categories to keep up with the most recent research. We review the literature of the last five years (2017-2021) and provide links to existing data and software resources. Finally, we survey recent works exploiting module identification and analysis, in the context of a variety of disease processes for biomarker identification and therapeutic target detection. Our review provides the interested reader with an up-to-date and self-contained view of the existing research, with links to state-of-the-art literature and resources, as well as hints on open issues and future research directions in complex detection and its applications.
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Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. FRONTIERS IN BIOINFORMATICS 2023; 3:1157956. [PMID: 36959975 PMCID: PMC10029925 DOI: 10.3389/fbinf.2023.1157956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.
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Affiliation(s)
- Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
- *Correspondence: Fotis A. Baltoumas, ; Nikos C. Kyrpides, ; Georgios A. Pavlopoulos,
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - David Paez-Espino
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
| | - Anastasis Oulas
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Robert D. Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, United States
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Nikos C. Kyrpides
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
- *Correspondence: Fotis A. Baltoumas, ; Nikos C. Kyrpides, ; Georgios A. Pavlopoulos,
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, Vari, Greece
- Center of New Biotechnologies and Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
- Hellenic Army Academy, Vari, Greece
- *Correspondence: Fotis A. Baltoumas, ; Nikos C. Kyrpides, ; Georgios A. Pavlopoulos,
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Tian C, Qiu M, Lv H, Yue F, Zhou F. Quantitative Proteomic Analysis of Serum Reveals MST1 as a Potential Candidate Biomarker in Spontaneously Diabetic Cynomolgus Monkeys. ACS OMEGA 2022; 7:46702-46716. [PMID: 36570245 PMCID: PMC9774375 DOI: 10.1021/acsomega.2c05663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
The prevalence of type 2 diabetes (T2DM) is increasing globally, creating essential demands for T2DM animal models for the study of disease pathogenesis, prevention, and therapy. A non-human primate model such as cynomolgus monkeys can develop T2DM spontaneously in an age-dependent way similar to humans. In this study, a data-independent acquisition-based quantitative proteomics strategy was employed to investigate the serum proteomic profiles of spontaneously diabetic cynomolgus monkeys compared with healthy controls. The results revealed significant differences in protein abundances. A total of 95 differentially expressed proteins (DEPs) were quantitatively identified in the current study, among which 31 and 64 proteins were significantly upregulated and downregulated, respectively. Bioinformatic analysis revealed that carbohydrate digestion and absorption was the top enriched pathway by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Protein-protein interaction network analysis demonstrated that MST1 was identified as the most connected protein in the network and could be considered as the hub protein. MST1 was significantly and inversely associated with FSG and HbA1c. Furthermore, recent lines of evidence also indicate that MST1 acts as a crucial regulator in regulating hepatic gluconeogenesis to maintain metabolic homeostasis while simultaneously suppressing the inflammatory processes. In conclusion, our study provides novel insights into serum proteome changes in spontaneously diabetic cynomolgus monkeys and points out that the dysregulation of several DEPs may play an important role in the pathogenesis of T2DM.
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Affiliation(s)
- Chaoyang Tian
- Key
Laboratory of Biomedical Engineering of Hainan Province, School of
Biomedical Engineering, Hainan University, Haikou, Hainan 570228, China
- One
Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Mingyin Qiu
- Animal
Experiment Department, Hainan Jingang Biotech
Co., Ltd., Haikou, Hainan 571100, China
| | - Haizhou Lv
- Animal
Experiment Department, Hainan Jingang Biotech
Co., Ltd., Haikou, Hainan 571100, China
| | - Feng Yue
- Key
Laboratory of Biomedical Engineering of Hainan Province, School of
Biomedical Engineering, Hainan University, Haikou, Hainan 570228, China
- One
Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Feifan Zhou
- Key
Laboratory of Biomedical Engineering of Hainan Province, School of
Biomedical Engineering, Hainan University, Haikou, Hainan 570228, China
- One
Health Institute, Hainan University, Haikou, Hainan 570228, China
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Anatolou D, Dovrolis N, Ragia G, Kolios G, Manolopoulos VG. Unpacking COVID-19 Systems Biology in Lung and Whole Blood with Transcriptomics and miRNA Regulators. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:608-621. [PMID: 36269619 DOI: 10.1089/omi.2022.0104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
COVID-19 is a systemic disease affecting tissues and organs, including and beyond the lung. Apart from the current pandemic context, we also have vastly inadequate knowledge of consequences of repeated exposures to SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus causing COVID-19, in multiple organ systems and the whole organism scales when the disease evolves from a pandemic to an endemic state. This calls for a systems biology and systems medicine approach and unpacking the effects of COVID-19 in lung as well as other tissues. We report here original findings from transcriptomics analyses and differentially expressed genes (DEGs) in lung samples from 60 patients and 27 healthy controls, and in whole blood samples from 255 patients and 103 healthy individuals. A total of 11 datasets with RNA-seq transcriptomic data were obtained from the Gene Expression Omnibus and the European Nucleotide Archive. The identified DEGs were used to construct protein interaction and functional networks and to identify related pathways and miRNAs. We found 35 DEGs common between lung and the whole blood, and importantly, 2 novel genes, namely CYP1B1 and TNFAIP6, which have not been previously implicated with COVID-19. We also identified four novel miRNA potential regulators, hsa-mir-192-5p, hsa-mir-221-3p, hsa-mir-4756-3p, and hsa-mir-10a-5p, implicated in lung or other diseases induced by coronaviruses. In summary, these findings offer new molecular leads and insights to unpack COVID-19 systems biology in a whole organism context and might inform future antiviral drug, diagnostics, and vaccine discovery efforts.
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Affiliation(s)
- Dimitra Anatolou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Nikolas Dovrolis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Georgia Ragia
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Vangelis G Manolopoulos
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
- Clinical Pharmacology Unit, Academic General Hospital of Alexandroupolis, Alexandroupolis, Greece
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49
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Nucleotide-based genetic networks: Methods and applications. J Biosci 2022. [PMID: 36226367 PMCID: PMC9554864 DOI: 10.1007/s12038-022-00290-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genomic variations have been acclaimed as among the key players in understanding the biological mechanisms behind migration, evolution, and adaptation to extreme conditions. Due to stochastic evolutionary forces, the frequency of polymorphisms is affected by changes in the frequency of nearby polymorphisms in the same DNA sample, making them connected in terms of evolution. This article presents all the ingredients to understand the cumulative effects and complex behaviors of genetic variations in the human mitochondrial genome by analyzing co-occurrence networks of nucleotides, and shows key results obtained from such analyses. The article emphasizes recent investigations of these co-occurrence networks, describing the role of interactions between nucleotides in fundamental processes of human migration and viral evolution. The corresponding co-mutation-based genetic networks revealed genetic signatures of human adaptation in extreme environments. This article provides the methods of constructing such networks in detail, along with their graph-theoretical properties, and applications of the genomic networks in understanding the role of nucleotide co-evolution in evolution of the whole genome.
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Lai JW, Cheong KH. A comprehensive framework for preference aggregation Parrondo's paradox. CHAOS (WOODBURY, N.Y.) 2022; 32:103107. [PMID: 36319284 DOI: 10.1063/5.0101321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Individuals can make choices for themselves that are beneficial or detrimental to the entire group. Consider two losing choices that some individuals have to make on behalf of the group. Is it possible that the losing choices combine to give a winning outcome? We show that it is possible through a variant of Parrondo's paradox-the preference aggregation Parrondo's paradox (PAPP). This new variant of Parrondo's paradox makes use of an aggregate rule that combines with a decision-making heuristic that can be applied to individuals or parts of the social group. The aim of this work is to discuss this PAPP framework and exemplify it on a social network. This work enhances existing research by constructing a feedback loop that allows individuals in the social network to adapt its behavior according to the outcome of the Parrondo's games played.
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Affiliation(s)
- Joel Weijia Lai
- Science, Mathematics and Technology Cluster, Singapore University of Technology and Design, 8 Somapah Road, S487372 Singapore
| | - Kang Hao Cheong
- Science, Mathematics and Technology Cluster, Singapore University of Technology and Design, 8 Somapah Road, S487372 Singapore
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